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A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

BACKGROUND: DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybr...

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Autores principales: Yu, Tianwei, Ye, Hui, Sun, Wei, Li, Ker-Chau, Chen, Zugen, Jacobs, Sharoni, Bailey, Dione K, Wong, David T, Zhou, Xiaofeng
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868765/
https://www.ncbi.nlm.nih.gov/pubmed/17477871
http://dx.doi.org/10.1186/1471-2105-8-145
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author Yu, Tianwei
Ye, Hui
Sun, Wei
Li, Ker-Chau
Chen, Zugen
Jacobs, Sharoni
Bailey, Dione K
Wong, David T
Zhou, Xiaofeng
author_facet Yu, Tianwei
Ye, Hui
Sun, Wei
Li, Ker-Chau
Chen, Zugen
Jacobs, Sharoni
Bailey, Dione K
Wong, David T
Zhou, Xiaofeng
author_sort Yu, Tianwei
collection PubMed
description BACKGROUND: DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required. RESULTS: We have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step. CONCLUSION: Using simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data.
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spelling pubmed-18687652007-05-15 A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array Yu, Tianwei Ye, Hui Sun, Wei Li, Ker-Chau Chen, Zugen Jacobs, Sharoni Bailey, Dione K Wong, David T Zhou, Xiaofeng BMC Bioinformatics Methodology Article BACKGROUND: DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required. RESULTS: We have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step. CONCLUSION: Using simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data. BioMed Central 2007-05-03 /pmc/articles/PMC1868765/ /pubmed/17477871 http://dx.doi.org/10.1186/1471-2105-8-145 Text en Copyright © 2007 Yu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Yu, Tianwei
Ye, Hui
Sun, Wei
Li, Ker-Chau
Chen, Zugen
Jacobs, Sharoni
Bailey, Dione K
Wong, David T
Zhou, Xiaofeng
A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
title A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
title_full A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
title_fullStr A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
title_full_unstemmed A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
title_short A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
title_sort forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (snp) array
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868765/
https://www.ncbi.nlm.nih.gov/pubmed/17477871
http://dx.doi.org/10.1186/1471-2105-8-145
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